Doomsday has killed Superman before, but he's been watered down significantly in recent years.
Darkseid too, was stronger than Superman and his Omega Beams are capable of wiping Superman from existance. But like Doomsday, Darkseid has been watered down quite a bit too.
In a straight fight, the Parasite would beat Superman every time. Of course, the true Parasite (Rudy) was killed off about 5 years ago and his replacement (Alexandra) is very easily defeated (a layer of clothing can stop her in her tracks).
With kryptonite powering him, Metallo has easily pounded Superman into the ground before. Without kryptonite, Metallo can still hold his own, usually with the help of some sort of gimmick (like his Cerberus/indestructible body, or the geo-magnet). Of course, Metallo's robot body has been taken from him recently, and he too is not really much of a threat anymore.
The Atomic Skull had strength on par with Superman, and he originally had invulnerability similar to Superman's when he was first introduced, but that power seems to have been retconned (and now it doesn't make sense that he can take a punch from Superman, but the force of a bullet's impact will take him out

). Unfortunately, the Skull was killed off a few months ago.
There are a number of other members of Superman's own rogues gallery who have a good chance of defeating Superman in a fight, but most of them have been forgotten by the current writers. And it seems that the few more well-known Superman villains who haven't been forgotten and once had a strong chance of beating him (listed above) have been either watered down, killed off, or had their powers taken away.
Of course, there are always the characters who aren't necessary limited to Metropolis who have the potential to single-handedly defeat Superman, such as Dr. Fate, Captain Marvel, the Spectre, Zoom, the Flash, Mordru, and many others.